System and method for scanning and processing of payment documentation in an integrated partner platform

Embodiments of the present disclosure may be used to scan a check or other payment instrument into an image file and apply a credit to one or more invoices associated with the entity, such as invoices issued by a business partner of the entity originating the check. Where there are multiple invoices outstanding invoices, embodiments of the present disclosure can selectively apply credits to such invoices based on input from the entity and/or based on rules defining how such credit are to be applied to the invoices.